Extensive variation in virus-induced patterns of transposable element transcripts in Drosophila

Transposable elements (TEs) are widespread genomic parasites, whose activity is largely restrained by RNA interference pathways. Some of these pathways also contribute to antiviral immunity, allowing a mechanistic overlap that could generate interactions—or even trade-offs—between TE repression and viral defense. Here, we investigated this interplay by experimentally infecting two strains of Drosophila melanogaster and Drosophila simulans with three distinct viruses: Drosophila X virus (DXV), Flock House virus (FHV), and Invertebrate Iridescent virus 6 (IIV6). Through deep RNA-seq and small RNA-seq analyses, we show that viral infection consistently alters TE transcript abundance, although the direction and magnitude of these changes strongly depend on both the host strain and the virus. In addition, we provide an in-depth characterization of the dynamic TE repertoire that IIV6 carries. IMPORTANCE Transposable elements (TEs) are genomic parasites that are found in all genomes. Here, using two strains of Drosophila and three viruses, we show that viral infections consistently affect TE transcript amounts. However, the magnitude and direction of the TE modulation depend on the host strain, the virus, and the tissue. In addition, one of the viruses under study, the Invertebrate Iridescent virus 6 (IIV6), carries TEs on its own, which we characterize as a dynamic repertoire.